Question: edgeR Normalization Method
gravatar for p_das
3.7 years ago by
United States
p_das0 wrote:


Can anybody point out to a tutorial/paper which explains the normalization method used by edgeR?

Another thing, though, TMM is the default normalization method of edgeR, can one specify, any other normalization methods in edgeR?

Thank you!


edger • 3.8k views
ADD COMMENTlink modified 3.7 years ago by Ryan C. Thompson7.3k • written 3.7 years ago by p_das0

When I say TMM is excluding the Genome Biology TMM paper by Robinson and Oshlack...

ADD REPLYlink written 3.7 years ago by p_das0

What's wrong with the Genome Biology paper? That describes the TMM method called by calcNormFactors with its default settings. You're not going to get anything more descriptive than that.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Aaron Lun23k

Hi Aaron!

Nothing is wrong!! Just wanted to see if there are more write ups on TMM...No offense to the authors or the research group...


ADD REPLYlink written 3.7 years ago by p_das0

See Dillies et al. 2012 for a comparison of different normalization methods: 

edgeR's TMM and DESeq's method come out on top.


ADD REPLYlink written 3.7 years ago by Jenny Drnevich1.9k
Answer: edgeR Normalization Method
gravatar for Ryan C. Thompson
3.7 years ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.3k wrote:

The documentation for calcNormFactors describes the options for the method argument, which allows you to select 3 different normalization methods. In addition, you can calculate normalization factors by any method you like and store them in the DGEList object yourself under object$samples$norm.factors.

ADD COMMENTlink written 3.7 years ago by Ryan C. Thompson7.3k
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